Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
seqbias Resource Report Resource Website 10+ mentions |
seqbias (RRID:SCR_006832) | seqbias | software resource | Software package that implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
GNU Lesser General Public License | OMICS_01237, biotools:seqbias, BioTools:seqbias | https://bio.tools/seqbias, https://bio.tools/seqbias, https://bio.tools/seqbias | SCR_006832 | seqbias - Estimation of per-position bias in high-throughput sequencing data | 2026-08-01 12:03:13 | 30 | ||||||
|
eDMR Resource Report Resource Website 10+ mentions |
eDMR (RRID:SCR_006960) | eDMR | software resource | Comprehensive differentially methylated regions (DMR) analysis based on bimodal normal distribution model and weighted cost function for regional methylation analysis optimization. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
MIT License | biotools:edmr, OMICS_00622 | https://bio.tools/edmr | SCR_006960 | 2026-08-01 12:03:25 | 19 | |||||||
|
Peakzilla Resource Report Resource Website 1+ mentions |
Peakzilla (RRID:SCR_007471) | Peakzilla | software resource | An algorithm to identify transcription factor binding sites from ChIP-seq data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:peakzilla, OMICS_00454 | https://bio.tools/peakzilla | SCR_007471 | 2026-08-01 12:03:37 | 6 | ||||||||
|
RUM Resource Report Resource Website 1+ mentions |
RUM (RRID:SCR_008818) | RUM | software resource | An alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
OMICS_01249, biotools:rum | https://bio.tools/rum, https://github.com/itmat/rum/wiki | SCR_008818 | Rna seq Unified Mapper | 2026-08-01 12:04:04 | 7 | |||||||
|
QuasiRecomb Resource Report Resource Website 10+ mentions |
QuasiRecomb (RRID:SCR_008812) | QuasiRecomb | software resource | A jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data. | haplotype, next-generation sequencing, virus, parameter, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23383997 | OMICS_00229, biotools:quasirecomb | https://bio.tools/quasirecomb | SCR_008812 | QuasiRecomb - Probabilistic inference of viral Quasispecies | 2026-08-01 12:03:53 | 32 | ||||||
|
XPN Resource Report Resource Website 1+ mentions |
XPN (RRID:SCR_008845) | XPN | software resource | Merging Two Gene Expression Studies via Cross Platform Normalization. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
OMICS_00863, biotools:xpn | https://bio.tools/xpn | SCR_008845 | 2026-08-01 12:03:54 | 2 | ||||||||
|
MuSiC Resource Report Resource Website 100+ mentions |
MuSiC (RRID:SCR_008792) | MuSiC | software resource | A set of tools aimed at determining the significance of somatic mutations discovered within a given cohort of cancer samples, incorporating the cohort''s alignment data, variant lists and any relevant clinical data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Washington University in St. Louis; Missouri; USA |
PMID:22759861 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:MuSiC2, OMICS_00152 | https://bio.tools/MuSiC2, https://github.com/ding-lab/MuSiC2/blob/master/README.md | SCR_008792 | Mutational Significance In Cancer | 2026-08-01 12:03:37 | 485 | |||||
|
SeqSaw Resource Report Resource Website |
SeqSaw (RRID:SCR_009185) | SeqSaw | software resource | A package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21575597 | biotools:seqsaw, OMICS_01250 | https://bio.tools/seqsaw | SCR_009185 | SeqSaw - Short Spliced Sequence Mapping Tool | 2026-08-01 12:03:41 | 0 | ||||||
|
Supersplat Resource Report Resource Website 1+ mentions |
Supersplat (RRID:SCR_009826) | Supersplat | software resource | An application for discovering potential splice junctions in high throughput sequencing (HTS) data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01256, biotools:supersplat | https://bio.tools/supersplat | SCR_009826 | 2026-08-01 12:04:04 | 2 | ||||||||
|
SOAPsnp Resource Report Resource Website 100+ mentions |
SOAPsnp (RRID:SCR_010602) | SOAPsnp | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software providng a method based on Bayes? theorem (the reverse probability model) to call consensus genotype by carefully considering the data quality, alignment, and recurring experimental errors., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/gr.088013.108 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:soapsnp, OMICS_00078 | https://bio.tools/soapsnp, https://sources.debian.org/src/soapsnp/ | SCR_010602 | 2026-08-01 12:04:16 | 204 | ||||||
|
Crux tandem mass spectrometry analysis software Resource Report Resource Website 10+ mentions |
Crux tandem mass spectrometry analysis software (RRID:SCR_010648) | software resource | A software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification. Crux analyzes shotgun proteomics tandem mass spectra, associating peptides with observed spectra. This software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification is provided as a single executable. Crux is implemented in C and is distributed with source code freely to noncommercial users. Mass spectrometry, the core technology in the field of proteomics, promises to enable scientists to identify and quantify the entire complement of proteins in a complex biological sample. Currently, the primary bottleneck in this type of experiment is computational. Existing algorithms for interpreting mass spectra are slow and fail to identify a large proportion of the given spectra. We describe a database search program called Crux that reimplements and extends the widely used database search program Sequest. For speed, Crux uses a peptide indexing scheme to rapidly retrieve candidate peptides for a given spectrum. For each peptide in the target database, Crux generates shuffled decoy peptides on the fly, providing a good null model and, hence, accurate false discovery rate estimates. Crux also implements two recently described postprocessing methods: a p value calculation based upon fitting a Weibull distribution to the observed scores, and a semisupervised method that learns to discriminate between target and decoy matches. Both methods significantly improve the overall rate of peptide identification. | proteomics, software toolkit, source code, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: University of Washington; Seattle; USA |
PMID:18505281 DOI:10.1021/pr500741y |
nlx_66678, biotools:crux | https://bio.tools/crux | https://sources.debian.org/src/crux-toolkit/ | SCR_010648 | Crux | 2026-08-01 12:04:16 | 32 | ||||||
|
SNPinfo Web Server Resource Report Resource Website 100+ mentions |
SNPinfo Web Server (RRID:SCR_010589) | service resource | SNPinfo Web Server is a set of freely available web-based SNP selection tools where investigators can specify genes or linkage regions and select SNPs based on GWAS results, linkage disequilibrium (LD), and predicted functional characteristics of both coding and non-coding SNPs. The algorithm uses GWAS SNP P-value data and finds all SNPs in high LD with GWAS SNPs, so that selection is from a much larger set of SNPs than the GWAS itself. The program can also identify and choose tag SNPs for SNPs not in high LD with any GWAS SNP. We incorporate functional predictions of protein structure, gene regulation, splicing and miRNA binding, and consider whether the alternative alleles of a SNP are likely to have differential effects on function. Users can assign weights for different functional categories of SNPs to further tailor SNP selection. The program accounts for LD structure of different populations so that a GWAS study from one ethnic group can be used to choose SNPs for one or more other ethnic groups. SNP Selection and Functional Information *Candidate Gene SNP Selection (GenePipe):SNP selection for candidate genes based on Genome Wide Association Study (GWAS) results, functional SNP prediction and Linkage Disequilibrium (LD) information. *GWAS Functional SNP Selection (GenomePipe):Functional SNP selection from SNPs that are in high LD with GWAS SNPs *GWAS SNP Selection in Linkage Loci (LinkagePipe):GWAS SNP selection in candidate genomic regions (such as linkage loci) *LD TAG SNP Selection (TagSNP):LD tag SNP selection and visualization for single or multiple populations. Finalization of SNP list from various queries. *SNP Function Prediction (FuncPred): Querying SNP function predictions and ethnic-specific allele frequencies. *SNP Information in DNA Sequence (SNPseq):Visualization of SNP related information in the context of DNA sequence. Preparing DNA Sequence for PCR Primer Design considering SNP information. Detailed information of CpG region. | bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: National Institute of Environmental Health Sciences |
PMID:19417063 | nlx_46274, biotools:snpinfo | https://bio.tools/snpinfo | SCR_010589 | 2026-08-01 12:03:53 | 211 | ||||||||
|
SICER Resource Report Resource Website 100+ mentions |
SICER (RRID:SCR_010843) | SICER | software resource | A clustering software package for identification of enriched domains from histone modification ChIP-Seq data. | python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: George Washington University; Washington D.C.; USA |
PMID:19505939 | biotools:sicer, OMICS_00461 | https://bio.tools/sicer | SCR_010843 | SICER: A clustering approach for identification of enriched domains from histone modification ChIP-Seq data | 2026-08-01 12:04:17 | 409 | ||||||
|
MapSplice Resource Report Resource Website 100+ mentions |
MapSplice (RRID:SCR_010844) | MapSplice | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Accurate mapping of RNA-seq reads for splice junction discovery. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Kentucky; Kentucky; USA |
PMID:20802226 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mapsplice, OMICS_01243 | https://bio.tools/mapsplice | SCR_010844 | 2026-08-01 12:03:58 | 214 | ||||||
|
MIRA Resource Report Resource Website 1000+ mentions |
MIRA (RRID:SCR_010731) | MIRA | software resource | Sequence assembler and mapper for whole genome shotgun and EST/RNASeq sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge is required by: MITObim |
PMID:15140833 DOI:10.1101/gr.1917404 |
OMICS_00023, biotools:mira | https://bio.tools/mira | https://sources.debian.org/src/mira-assembler/ | SCR_010731 | Mimicking Intelligent Read Assembly | 2026-08-01 12:03:55 | 1036 | |||||
|
QSRA Resource Report Resource Website 1+ mentions |
QSRA (RRID:SCR_010733) | QSRA | software resource | A quality-value guided de novo short read assembler. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00026, biotools:qsra | https://bio.tools/qsra | SCR_010733 | 2026-08-01 12:04:16 | 1 | ||||||||
|
HARSH Resource Report Resource Website 10+ mentions |
HARSH (RRID:SCR_010792) | HARSH | software resource | Software that provides a method to infer the haplotype using haplotype reference panel and high throughput sequencing data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Los Angeles; California; USA |
OMICS_00199, biotools:harsh | https://bio.tools/harsh | SCR_010792 | HAplotype inference using Reference and Sequencing tecHnology | 2026-08-01 12:04:17 | 15 | |||||||
|
HapFABIA Resource Report Resource Website 1+ mentions |
HapFABIA (RRID:SCR_010793) | HapFABIA | software resource | Software that identifies short identity by descent (IBD) segments that are tagged by rare variants in large sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Johannes Kepler University of Linz; Linz; Austria |
PMID:24174545 | biotools:hapfabia, OMICS_00203 | https://bio.tools/hapfabia | SCR_010793 | HapFABIA: Identification of very short segments of identity by descent characterized by rare variants in large sequencing data | 2026-08-01 12:03:57 | 3 | ||||||
|
Pedimap Resource Report Resource Website 10+ mentions |
Pedimap (RRID:SCR_010796) | Pedimap | software resource | A software tool for visualizing phenotypic and genotypic data for related individuals linked in pedigrees. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23087384 | OMICS_00214, biotools:pedimap | https://bio.tools/pedimap | SCR_010796 | 2026-08-01 12:04:17 | 11 | |||||||
|
CEQer Resource Report Resource Website 1+ mentions |
CEQer (RRID:SCR_010813) | CEQer | software resource | A graphical, event-driven tool for CNA/AI-coupled analysis of exome sequencing reads. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24124457 | Commercial license, Free | biotools:ceqer, OMICS_00329 | https://bio.tools/ceqer | SCR_010813 | Comparative Exome Quantification analyzer | 2026-08-01 12:04:16 | 7 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
